NOTE - see bottom of page for previous weeks' schedules and things to catch up on.
Definitions: 'cubby' = VDS cabinet in back of lab where all of our reagents are; 'pigeon hole' = the shelf for your lab notebook over by the window. Daily Schedule Summ14Timeline F13
This also has the Presentation Guidelines for all 3 types of presentations: Research Presentations, Technical Presentations, Journal Club Presentations
Link to Research Progress Table
Wikispaces check on every other Sunday (Bi-weekly)
Class slides are uploaded to CANVAS after each class.
This Week
This Week
WEEK15 - final week
Peer Reviews - should already have these done
Peer Review of Research Report on Target (Mid semester) - 1 per person
Peer Review of M&M Cloning - 2 per person
Peer Review of M&M Virtual- 2 per person
SKIP: peer review of M&M Expr, Pur, Char
Wet Lab work
finish cloning
express a FtHap protein if finished with at least 3 cloning attempts
Virtual Work
- analyze scores
---InHouseCompounds (~40 ligs) -use 1 processor
---CB306 (306 ligs) - use 1 processor
---NIHClinicalCollection (446 ligs), use 1 processor
---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor
4-Dec Thursday
Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard 5-Dec Friday
Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard 6-Dec Saturday
Final Lab Report Due @ 9pm
7-Dec Sunday
Wikispaces posting due - Sundays at 9 pm (For Weeks 14, 15)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y'
Monday Dec 8th -
Final Lab Notebook Due at 9pm
WEEK15 - final week
Peer Reviews - should already have these done
Peer Review of Research Report on Target (Mid semester) - 1 per person
Peer Review of M&M Cloning - 2 per person
Peer Review of M&M Virtual- 2 per person
SKIP: peer review of M&M Expr, Pur, Char
Enzyme Assays & Inhibition Assays
determine if your enzyme is active
determine how much enzyme to use to get 'good' absorbance signal
4-Dec Thursday
Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard 5-Dec Friday
Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard 6-Dec Saturday
Final Lab Report Due @ 9pm
7-Dec Sunday
Wikispaces posting due - Sundays at 9 pm (For Weeks 14, 15)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y'
Monday Dec 8th -
Final Lab Notebook Due at 9pm
SPRINGERS
VETERANS
Next Week
Next Week
RECURRING ITEMS:
Wikispaces posting due - Sundays at 9 pm
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y' Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Wiki postings should be a sort of highlights of results page.
You should have nanodrop images, gel images, yields from protein purification, brief virtual results, etc.
You don't need alot of lengthy description of the procedures - only figure captions and a brief analysis of
the result (e.g. 1-2 sentences of why it did or didn't work, next steps, etc.).
You should have enough information in the captiont to let the reader (Dr. B) understand what it is.
Lab Notebook check - Saturdays at 5pm
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.
DNA Works Output file - print the text file and past in notebook
Tail Primer Design (protocol and what you designed)
Info from your Target Page (which means you need a Target page first!)
Update Target page on Wikispaces (need all the info from the list of items)
- if you don't have a Target page - start making it for your Target .
ITEMS FOR LATER:
Cut pNIC-Bsa4 that you grew up with BsaI (part of pNIC-Bsa4 Cloning protocol), gel check
Tail Primer Design and Ordering
Make LB+Kan plates (4) -
ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)
Make LB + Kan/Suc plates (6)
ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)
After Fire Safety Training is uploaded: PAPER COPY – Print out of TxClass Safety Training - - (can put in Safety section of VDS sign-in binder in lab)
Project Tasks (in rough order):
Nanodrop & Submit to DNA Sequencing (1.5 hrs)
Target Selection Form
Dilute some primers from lyophilized powder: random ones (pLIC-for & pLIC-rev)?
-- make working dilution in water from 100uM stock.
-- Store working dilution in YOUR own box.
Make 500ml of LB and autoclave (with mentor) Transform pNIC-Bsa4 into DH5alpha (with a partner) - use 'homemade' competent cells (NOT THE NEB ones) ---- ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v5
Graded Assignments: HOURS:
Week1&2 Hrs
Week 3&4 Hrs
......
LabNotebook A, B, C, D
Wikispaces (Bi-Weekly)
WikiWeek1&2
Safety
Target Page
LICpNIC-Bsa4cloningExercise
Journal Club presentation and Question sheets
Technical Presentation (if applicable)
Research Presentation
PyMol Refresher
Virtual Screening Refresher
Mid-Semester Research Report on Target
Draft of M&M Cloning
Draft of M&M Virtual
Draft of M&M Express,Pur,Char
Final Report
Everyone designs their primer - but we will only order one person's set.
Be sure you use the correct DNA Works output file to get your codon optimized DNA sequence (not just the CDS).
-- If you are use a Summer plate - you need to get your DNA Works Output file from Misc/Primers/DNAWorks_OutputSummer14
-- If you are use a Fall plate - you need to get your DNA Works Output file from Misc/Primers/DNAWorks_OutputFall14
Save the Word doc of your primer design into your GDocs
Print Word doc and paste into your Lab Notebook
Crosscheck your sequence with your Teammates
Put the sequences of the Tail Primers on your team's target page.
-- Enter your name for the person whose primers we will order - once you have designed the primers
Put the info and sequence on the Target Spreadsheet
Order your primers
-- go to the ICMB core site (see our Targets Spreadsheet for the link)
-- find the IDT link
-- enter our username: VDS (all caps) and password: same as the password to get on to the laptops buildingname+labroomnumber
--Products/DNA/RNASynthesis/CustomDNAOligos
--select 2 for the Multiple Entry
-- leave defaults for Scale and Purification
-- enter your 2 primers and the Prefixes.
-- save to Wishlist, Dr. B will order when we have several of them.
WEEK1 25-Aug Monday 26-Aug Tuesday 27-Aug Wednesday
class 28-Aug Thursday
sign up for Fire Safety training (see link to left 'Required Lab Safety')
Lab times open for Nanodrop and Submit to DNA sequencing
WEEK1
25-Aug Monday
26-Aug Tuesday
27-Aug Wednesday class
28-Aug Thursday sign up for Fire Safety training (see link to left 'Required Lab Safety') startup your cloning work again
29-Aug Friday
30-Aug Saturday
31-Aug Sunday
SPRINGERSWEEK2
Be sure you have 8-10hrs/week - for the 1st week of class that should be about 3-4hrs since the lab was only open for 2 days For this week, you need about 6.5-8 hrs.
ITEMS TO DO THIS WEEK**
sign up for Fire Safety training (see link to left 'Required Lab Safety')
Create your own folder in Google Docs under the folder: /StudentFolders
Make 500ml of LB and autoclave (with mentor) - anytime mentor available
Transform pNIC-Bsa4 into DH5alpha (with a partner) - use 'homemade' competent cells (NOT THE NEB ones) - at specific times
Dilute some primers (if they come in) - anytime mentor available
Target Selection Form - once Dr. B sends the link
Analyze DNA Sequence Exercise (as a group) - at specific times (this week or next depending on Target Selections and Primer Design)
(maybe) RE Digest - at specific times
1-Sep Monday - LABOR DAY - no lab 2-Sep Tuesday
Transformation times at 3:30 PM (must start on time) Make 500ml of LB and autoclave (with mentor)
3-Sep Wednesday
class
Transformation times at 3:30 PM (must start on time) Make 500ml of LB and autoclave (with mentor)
4-Sep Thursday
Make 500ml of LB and autoclave (with mentor) Dilute some primers (if they come in) Transformation times at 5:30 PM (must start on time)
5-Sep Friday
1:30-4:30 pm Analyze DNA Sequence Exercise (as a group) OR Primer Design if Targets figured out Make 500ml of LB and autoclave (with mentor) Dilute some primers (if they come in)
6-Sep Saturday Lab Notebook check - Saturday at 5pm
What Goes Where for notebook?:
Nanorop - 2 images for Wiki & protocol/images in Notebook
Submit to DNA - protocol in Notebook, if have result - put in Notebook too
Wet lab and virtual work should go into notebook
Oligo Design - upload output file to GDocs, paste Oligo sequence into your Target page, in Notebook too
Analyze DNA Sequence - upload results to GDocs (put the protocol in your Notebook - results can stay in GDocs)
RE Digest - if done
PCR & run on an agarose gel - images to Wiki & protocol/images in Notebook
7-Sep Sunday
Target page updates due - 9 pm - SKIP FOR THIS WEEK
Wikispaces posting due - 9 pm
Add content to YOUR research page on Wikispaces
Put a line and 'Week 1&2' Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Wiki postings should be a sort of highlights of results page.
You should have nanodrop images, gel images, yields from protein purification, brief virtual results, etc.
You don't need alot of lengthy description of the procedures - only figure captions and a brief analysis of
the result (e.g. 1-2 sentences of why it did or didn't work, next steps, etc.).
You should have enough information in the captiont to let the reader (Dr. B) understand what it is.
WEEK2 Be sure you have 8-10hrs/week
- for the 1st week of class that should be about 3-4hrs since the lab was only open for 2 days
For this week, you need about 6.5-8 hrs.
1-Sep Monday 2-Sep Tuesday 3-Sep Wednesday
class
3-4 Zain & Hailey site specific training with Priya
4-Sep Thursday 5-Sep Friday
6-Sep Saturday 7-Sep Sunday
WEEK3
ITEMS TO DO THIS WEEK
RE Digest of pGBR22
ProtocolRestrictionEnzymeDigestVDS.doc
Dilute some primers (if they come in) - anytime mentor available
Grow up your pNIC-Bsa4 colonies (DH5alpha) overnight
If failed last week, Re-transform pNIC-Bsa4 into DH5alpha (with a partner)
- use 'homemade' competent cells (NOT THE NEB ones) - at specific times
Target Selection Form - once Dr. B sends the link - SENT
Primer Design and Ordering
Create/Update Target pages
MAYBE: 'My First PCR' - using pGBR22
- ProtocolPCRVDS.xls
Grow up DH5alpha cells for Plasmid Preps (just store pellets though - don't do MidiPrep yet):
4:00 - 5 PM - start overnight cultures of plasmids in DH5alpha for midi prepping later.
-Grow up pNIC-Bsa4 overnight in 160ml of LB + Kan
--pNIC-Bsa4 is a 'low copy' plasmid
--spin down next morning
(save in -20degC or proceed to Midi-Prep - 2-3hrs)
-- if you don't' have time to spin down in morning (~30-45 min), you can
temporarily store your growth flask in 4degC for a few hours til you can spin it in the afternoon.
Pellets can be frozen and stored til next day or so.
In order to make lots of plasmid that we will need for cloning:
-- Plasmid Midi-prep (in pairs) - use Tony's new protocol
8-Sep Monday 9-Sep Tuesday FIRE SAFETY TRAINING for FRI Students only -- Speed Way in front of SAC (just show up and sign in)
Create/Update Target page on Wikispaces for your Team's target
Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall14.doc - 2 hrs
upload final primers to Google Docs/VDS/Misc/Primers/PrimerPlateOrderFall2014
post final primers to Wikispaces Target page
12-SepFriday
Create/Update Target page on Wikispaces for your Team's target
Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall14.doc - 2 hrs
upload final primers to Google Docs/VDS/Misc/Primers/PrimerPlateOrderFall2014
post final primers to Wikispaces Target page
13-SepSaturday 14-SepSunday
WEEK3 8-Sep Monday 9-Sep Tuesday FIRE SAFETY TRAINING for FRI Students only -- Speed Way in front of SAC (just show up and sign in)
10-SepWednesday
class
11-SepThursday
4- 8 pm PyMol Refresher Help Session in Computer Lab
12-SepFriday
PyMol Refresher due for Vets (less Zain, Hailey)
can count as 2 hours of lab time
13-SepSaturday 14-SepSunday
WEEK4
ITEMS TO DO THIS WEEK
Run gel of RE Digest of pGBR22
Agarose Gel protocol
Grow up your pNIC-Bsa4 colonies (DH5alpha) overnight (see below for steps)
Target Page - update yours with your team (the person who comes first on the list of names is the point person and delegates the work)
'My First PCR' - using pGBR22
- ProtocolPCRVDS.xls
PyMol Refresher
Grow up pNIC-Bsa4 in DH5alpha cells for Plasmid Preps
4:00 - 5 PM - start overnight cultures of plasmids in DH5alpha for midi prepping later.
-Grow up pNIC-Bsa4 overnight in 160ml of LB + Kan
--pNIC-Bsa4 is a 'low copy' plasmid
--spin down next morning (10-11 am) - make sure a mentor can be there!
(save in -20degC or proceed to Midi-Prep - 2-3hrs)
-- if you don't' have time to spin down in morning (~30-45 min), you can
temporarily store your growth flask in 4degC for a few hours til you can spin it in the afternoon.
Pellets can be frozen and stored til next day or so.
Not due yet, but Mid Semester Research Report Guidelines posted to:
GDocs/Results&Data/ResearchReport/
GuidelinesResearchReportonTarget_VDS_Fall14.doc
What Goes Where for notebook?:
Oligo Design - protocol and DNA Works output file
Analyze DNA Sequence
RE Digest
PCR & run on an agarose gel (if done)
21-SepSunday
Wikispaces posting due - 9 pm
Add content to YOUR research page on Wikispaces
Put a line and 'Week 3&4' Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Wiki postings should be a sort of highlights of results page.
You should have nanodrop images, gel images, yields from protein purification, brief virtual results, etc.
You don't need alot of lengthy description of the procedures - only figure captions and a brief analysis of
the result (e.g. 1-2 sentences of why it did or didn't work, next steps, etc.).
You should have enough information in the caption to let the reader (Dr. B) understand what it is.
You don't have to do all of these protocols right away - but you should aim to have your Homology model created this week and have started on Control Ligands selection (the first part of the Virtual Screening Protocol).
-- see the sign up spreadsheet above for times
Target Page - update yours with your team (the person who comes first on the list of names is the point person and delegates the work)
Not due yet, but Mid Semester Research Report Guidelines posted to:
GDocs/Results&Data/ResearchReport/
GuidelinesResearchReportonTarget_VDS_Fall14.d
22-SepMonday 23-SepTuesday 24-SepWednesday
Virtual Screening Refresher due for Vets
can count as 2 hours of lab time
(Zain & Hailey) do PyMol Refresher
5-Oct Sunday Mid Semester Research Report due (a.k.a. Report on your Target)
Guidelines posted to:
GDocs/Results&Data/ResearchReport/GuidelinesResearchReportonTarget_VDS_Fall14.doc
WEEK6 Cloning should be completed by end or September Start Expression
Virtual Work
Control Ligands selection and LigPrep is due at end of week
Beginning of the ProtocolVirtualScreenYOURTarget_VDS_Fall14.doc
5-Oct Sunday Mid Semester Research Report due (a.k.a. Report on your Target)
Guidelines posted to:
GDocs/Results&Data/ResearchReport/GuidelinesResearchReportonTarget_VDS_Fall14.doc
WEEK7
Check the Mentor schedule to see when mentors
will be present in lab to help you out.
Wet Lab
Primary PCR trials
ProtocolPCR_PrimerOverlap
WithQ5Polymerase_VDS_Fall14.docx
Primer Dilution of your own tail primers
Secondary PCR trials
Virtual Work
Virtual Screening Refresher - due in 2 weeks from now
Wikispaces posting due - Sundays at 9 pm (For Weeks 5,6,7)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y&Z'
WEEK8
Check the Mentor schedule to see when mentors will be present in lab to help you out.
We will also have some dedicated virtual screening help sessions (see below)
Wet Lab
continue cloning work on your project
start cutting your pNIC-Bsa4 while working on your PCRs
Virtual Work * Virtual Screening Refresher (can count as 4 hrs of wet lab time for the whole exercise)
13-OctMonday
5-7 pm Virtual Screening Help Session in wet lab 14-OctTuesday 15-OctWednesday
3-7 pm Virtual Screening Help Session in wet lab
16-OctThursday
4-7 pm Help Session for:
Virtual Screening & LICpNIC-Bsa4cloningExercise
17-OctFriday
2-6 PM Help Session for:
Virtual Screening & LICpNIC-Bsa4cloningExercise
Check the Mentor schedule to see when mentors will be present in lab to help you out.
We will also have some dedicated virtual screening help sessions (see below)
Wet Lab
continue cloning work on your project
start cutting your pNIC-Bsa4 while working on your PCRs
once PCR Squared is done - carry out cloning protocol
ProtocolpNIC-Bsa4_cloningVDS_Fall14.doc
make sucrose + kan plates if there aren't any (get a mentors help)
Virtual Work
* Virtual Screening Refresher (can count as 4 hrs of wet lab time for the whole exercise)
20-OctMonday
21-OctTuesday 22-OctWednesday 23-OctThursday 24-OctFriday 25-OctSaturday
Virtual Screening Refresher - due
26-OctSunday
Peer Review of Mid Semester Research Report on target
--- see GDrive folder for instructions (
ResearchReport_Materials&Methods_Guidelines)
WEEK9
Wet Lab
purchase your substrates with Dr. B (if you have not already done so)
enzyme assays - does your enzyme work?
Virtual Work
- analyze scores
- submit jobs for a large screening library (CB Diversity - 50k)
only use ~ 6 processors so that everyone can run their jobs
Peer Review of Mid Semester Research Report on target
--- see GDrive folder for instructions (
ResearchReport_Materials&Methods_Guidelines)
WEEK10
Check the Mentor schedule to see when mentors will be present in lab to help you out.
We will also have some dedicated virtual screening help sessions (see below)
Wet Lab
continue cloning work on your project
carry out cloning protocol
ProtocolpNIC-Bsa4_cloningVDS_Fall14.doc
make sucrose + kan plates if there aren't any (get a mentors help)
Virtual Work
Control Ligands selection and LigPrep
Virtual Set up
Submit docking job of control ligands
27-OctMonday 28-OctTuesday 29-OctWednesday - Journal Club 30-OctThursday 31-OctFriday 1-Nov Saturday
Lab Notebook Due at 5pm
2-Nov Sunday
Cloning Materials & Methods due
Wikispaces posting due - Sundays at 9 pm (For Weeks 8,9,10)
Add content to YOUR research page on Wikispaces
Put a line and 'Week 8, 9, and 10'
27-OctMonday 28-OctTuesday 29-OctWednesday - Journal Club 30-OctThursday 31-OctFriday 1-Nov Saturday
Lab Notebook Due at 5pm
2-Nov Sunday
Cloning Materials & Methods due
Wikispaces posting due - Sundays at 9 pm (For Weeks 8,9,10)
Add content to YOUR research page on Wikispaces
Put a line and 'Week 8, 9, and 10'
WEEK11
Check the Mentor schedule to see when mentors will be present in lab to help you out.
We will also have some dedicated virtual screening help sessions (see below)
Wet Lab
continue cloning work on your project
carry out cloning protocol
ProtocolpNIC-Bsa4_cloningVDS_Fall14.doc
make sucrose + kan plates if there aren't any (get a mentors help)
Virtual Work
Control Ligands selection
ProtocolVirtualScreenYOURTarget_VDS_??.doc (first part only for now = Control Ligand Selection)
Peer Review of M&M Cloning Due at m/n -
–You have 2 different people’s which you need to review
–Make 5 constructive criticisms
–Make 2 compliments
- make sure to add your Initials to each comment so we know who did what - JTB
Peer Review of M&M Cloning Due at m/n
–You have 2 different people’s which you need to review
–Make 5 constructive criticisms
–Make 2 compliments
- make sure to add your Initials to each comment so we know who did what - JTB
WEEK12
Virtual Work
Control Ligands - LigPrep
Protocol_LigandPrep_VDS_v1.docx
Virtual Set up
ProtocolVirtualScreenYOURTarget_VDS.doc
create homology model if needed for your target
ProtocolHomologyModelVDS_v.doc
Submit docking job of control ligands
Virtual Work
- analyze control ligands' scores
- submit jobs for small screening libraries (cb306, NIHcc, HF9)
---InHouseCompounds (~40 ligs) -use 1 processor
---CB306 (306 ligs) - use 1 processor
---NIHClinicalCollection (446 ligs), use 1 processor
---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor
10-NovMonday 11-NovTuesday 12-NovWednesday
no journal club this week 13-Nov Thursday 14-Nov Friday 15-NovSaturday 16-NovSunday
Virtual M&M due
Enzyme Assays
determine is your enzyme is active
determine how much enzyme to use to get 'good' absorbance signal
vary amount of substrates(s) to optimize assay
Virtual Work
- analyze control ligands' scores
- submit jobs for small screening libraries (cb306, NIHcc, HF9)
---InHouseCompounds (~40 ligs) -use 1 processor
---CB306 (306 ligs) - use 1 processor
---NIHClinicalCollection (446 ligs), use 1 processor
---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor
--- If those look good - submit CBDiversity (large library - ~50k)
WEEK12 10-NovMonday 11-NovTuesday 12-NovWednesday
no journal club this week 13-Nov Thursday 14-Nov Friday 15-NovSaturday 16-NovSunday
Virtual M&M due
WEEK13
Virtual Work
- analyze scores
- continue screening small screening libraries (cb306, NIHcc, HF9)
---InHouseCompounds (~40 ligs) -use 1 processor
---CB306 (306 ligs) - use 1 processor
---NIHClinicalCollection (446 ligs), use 1 processor
---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor
17-Nov Monday 18-Nov Tuesday 19-Nov Wednesday
Journal Club
20-Nov Thursday 21-Nov Friday 22-Nov Saturday
Lab Notebook Due at 5pm
23-Nov Sunday
Wikispaces posting due - Sundays at 9 pm (For Weeks 11,12,13)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y&Z'
WEEK13
Enzyme Assays & Inhibition Assays
determine if your enzyme is active
determine how much enzyme to use to get 'good' absorbance signal
vary amount of substrates(s) to optimize assay
Dilute inhibitors in DMSO
test out inhibitors (vary concentration)
Virtual Work
- analyze scores for ChemBridge Diversity
17-Nov Monday 18-Nov Tuesday 19-Nov Wednesday
Journal Club
20-Nov Thursday 21-Nov Friday 22-Nov Saturday
Lab Notebook Due at 5pm
23-Nov Sunday
Wikispaces posting due - Sundays at 9 pm (For Weeks 11,12,13)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y&Z'
Virtual Work
do some virtual screening
Wet Lab work
we will have mentors on duty for Mon, Tues, Wed - so continue your cloning work if you are in town
WEEK14 24-Nov Monday
25-Nov Tuesday -
Peer Review of M&M Virtual Due at m/n –You have 2 different people’s which you need to review –Make 5 constructive criticisms –Make 2 compliments - make sure to add your Initials to each comment so we know who did what - JTB
Expression, Purification, Characterization M&M due (can also turn in on Sunday night (Nov 30th)
It may be part of your proposed methods – but it still must be detailed.
I want you to think about the process and be able to explain the concepts.
You have done a somewhat similar Expression, Purification & Characterization in spring
26-Nov Wednesday - NO CLASS (Thanksgiving Break)
We will have mentors on duty if you want to do lab work
27-Nov Thursday 28-Nov Friday 29-Nov Saturday 30-Nov Sunday
see above for Peer Review and M&M that are due
Virtual Work
do some virtual screening
Wet Lab work
we will have mentors on duty for Mon, Tues, Wed
WEEK14 24-Nov Monday
25-Nov Tuesday
Peer Review of M&M Virtual Due at m/n –You have 2 different people’s which you need to review –Make 5 constructive criticisms –Make 2 compliments - make sure to add your Initials to each comment so we know who did what - JTB
Expression, Purification, Characterization M&M due
(can also turn in on Sunday night (Nov 30th)
26-Nov Wednesday - NO CLASS (Thanksgiving Break)
We will have mentors on duty if you want to do lab work
27-Nov Thursday 28-Nov Friday 29-Nov Saturday 30-Nov Sunday see above for Peer Review and M&M that are due
TIMELINE FOR RESEARCH
NOTE - see bottom of page for previous weeks' schedules and things to catch up on.Definitions: 'cubby' = VDS cabinet in back of lab where all of our reagents are; 'pigeon hole' = the shelf for your lab notebook over by the window. Daily Schedule Summ14 Timeline F13
Looking for the Presentation Schedule? - see the Schedule Fall14 ( Semester)
- This also has the Presentation Guidelines for all 3 types of presentations: Research Presentations, Technical Presentations, Journal Club Presentations
Link to Research Progress TableWikispaces check on every other Sunday (Bi-weekly)
Class slides are uploaded to CANVAS after each class.
This Week
This Week
Peer Reviews - should already have these done
Wet Lab work
finish cloning
express a FtHap protein if finished with at least 3 cloning attempts
Virtual Work
1-Dec Monday
2-Dec Tuesday
3-Dec Wednesday
class
FRI Survey (10-20 min)
https://utexas.qualtrics.com/SE/?SID=SV_6G8NU0TAFlSWawJ
4-Dec Thursday
Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard
5-Dec Friday
Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard
6-Dec Saturday
Final Lab Report Due @ 9pm
7-Dec Sunday
Wikispaces posting due - Sundays at 9 pm (For Weeks 14, 15)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y'
Monday Dec 8th -
Final Lab Notebook Due at 9pm
Peer Reviews - should already have these done
Enzyme Assays & Inhibition Assays
Virtual Work
1-Dec Monday
2-Dec Tuesday
3-Dec Wednesday
class
FRI Survey (10-20 min)
https://utexas.qualtrics.com/SE/?SID=SV_6G8NU0TAFlSWawJ
4-Dec Thursday
Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard
5-Dec Friday
Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard
6-Dec Saturday
Final Lab Report Due @ 9pm
7-Dec Sunday
Wikispaces posting due - Sundays at 9 pm (For Weeks 14, 15)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y'
Monday Dec 8th -
Final Lab Notebook Due at 9pm
Next Week
Next Week
Wikispaces posting due - Sundays at 9 pm
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y'
Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Wiki postings should be a sort of highlights of results page.
You should have nanodrop images, gel images, yields from protein purification, brief virtual results, etc.
You don't need alot of lengthy description of the procedures - only figure captions and a brief analysis of
the result (e.g. 1-2 sentences of why it did or didn't work, next steps, etc.).
You should have enough information in the captiont to let the reader (Dr. B) understand what it is.
Lab Notebook check - Saturdays at 5pm
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.
Update Target page on Wikispaces (need all the info from the list of items)
- if you don't have a Target page - start making it for your Target .
ITEMS FOR LATER:
Cut pNIC-Bsa4 that you grew up with BsaI (part of pNIC-Bsa4 Cloning protocol), gel check
Tail Primer Design and Ordering
Make LB+Kan plates (4) -
ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)
Make LB + Kan/Suc plates (6)
ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)
After Fire Safety Training is uploaded:
PAPER COPY – Print out of TxClass Safety Training -
- (can put in Safety section of VDS sign-in binder in lab)
Project Tasks (in rough order):
Nanodrop & Submit to DNA Sequencing (1.5 hrs)
Target Selection Form
Dilute some primers from lyophilized powder: random ones (pLIC-for & pLIC-rev)?
-- make working dilution in water from 100uM stock.
-- Store working dilution in YOUR own box.
Make 500ml of LB and autoclave (with mentor)
Transform pNIC-Bsa4 into DH5alpha (with a partner) - use 'homemade' competent cells (NOT THE NEB ones)
---- ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v5
Midi-prep (in pairs) - use Tony's new protocol
Input information about which culture of plasmid you have (or will) grow up.
GoogleDocs/Misc/Plasmid Concentrations
https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
Submit to DNA Sequencing for YOUR pNIC-Bsa4 that you grew up
Analyze DNA Sequence Exercise (as a group)
Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall14.doc - 2 hrs
'My Second PCR' - PCR pLIC using pNIC-Bsa4
Set up target protein for Virtual Screening
Design Tail Primers for targets, order tail primers
Primer Dilution or your own primers
Create or Revise your Target page (not same as you Research Page)
LICpNIC-Bsa4cloningExerciseVDS_Fall14
Make Oligo mix for Targets
Expression
Purification
Characterization
PROTEIN INFO
Enter your protein yields into: Protein Spectrophotometer Calc
https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodC1mRVpNLVlDOUE4NlNxdldqNEZwRmc&usp=sharing
Virtual Work
CB Diversity (50K ligs) screening Due
M&M's
Cloning Materials & Methods due @ ???
-- see guidelines on GDocs
Peer Review of M&M Cloning is due @ ???
- you will have 2 to review
- make 5 constructive criticisms
- make 2 compliments
Virtual M&M due @ ???
Expression, Purification, Characterization M&M due @ ???
-- see guidelines on GDocs
Peer Review due ??:
M&M Virtual
Peer Review due ??:
M&M Expression, Pur, Char
Finish virtual screening
Enzyme Assay protocol
Inhibition Assay protocol
Graded Assignments:
HOURS:
Week1&2 Hrs
Week 3&4 Hrs
......
LabNotebook A, B, C, D
Wikispaces (Bi-Weekly)
WikiWeek1&2
Safety
Target Page
LICpNIC-Bsa4cloningExercise
Journal Club presentation and Question sheets
Technical Presentation (if applicable)
Research Presentation
PyMol Refresher
Virtual Screening Refresher
Mid-Semester Research Report on Target
Draft of M&M Cloning
Draft of M&M Virtual
Draft of M&M Express,Pur,Char
Final Report
2 Weeks Blocks layout
WEEK2
WEEK3
WEEK4
WEEK5
WEEK6
WEEK7
WEEK8
WEEK9
WEEK10
WEEK11
WEEK12
WEEK13
WEEK14
WEEK15
9-Dec Tuesday
10-DecWednesday
11-DecThursday
12-DecFriday
13-DecSaturday
14-DecSunday
15-DecMonday
16-DecTuesday
9-Sep Tuesday
10-SepWednesday
11-SepThursday
12-SepFriday
13-SepSaturday
14-SepSunday
15-SepMonday
16-SepTuesday
17-SepWednesday
18-SepThursday
19-SepFriday
20-SepSaturday
21-SepSunday
22-SepMonday
23-SepTuesday
24-SepWednesday
25-SepThursday
26-SepFriday
27-SepSaturday
28-SepSunday
29-SepMonday
30-SepTuesday
1-Oct Wednesday
2-Oct Thursday
3-Oct Friday
4-Oct Saturday
5-Oct Sunday
6-Oct Monday
7-Oct Tuesday
8-Oct Wednesday
9-Oct Thursday
10-OctFriday
11-OctSaturday
12-OctSunday
13-OctMonday
14-OctTuesday
15-OctWednesday
16-OctThursday
17-OctFriday
18-OctSaturday
19-OctSunday
20-OctMonday
21-OctTuesday
22-OctWednesday
23-OctThursday
24-OctFriday
25-OctSaturday
26-OctSunday
27-OctMonday
28-OctTuesday
29-OctWednesday
30-OctThursday
31-OctFriday
1-Nov Saturday
2-Nov Sunday
3-Nov Monday
4-Nov Tuesday
5-Nov Wednesday
6-Nov Thursday
7-Nov Friday
8-Nov Saturday
9-Nov Sunday
10-Nov Monday
11-Nov Tuesday
12-Nov Wednesday
13-Nov Thursday
14-Nov Friday
15-Nov Saturday
16-Nov Sunday
17-Nov Monday
18-Nov Tuesday
19-Nov Wednesday
20-Nov Thursday
21-Nov Friday
22-Nov Saturday
23-Nov Sunday
24-Nov Monday
25-Nov Tuesday
26-Nov Wednesday
27-Nov Thursday
28-Nov Friday
29-Nov Saturday
30-Nov Sunday
1-Dec Monday
2-Dec Tuesday
3-Dec Wednesday
4-Dec Thursday
5-Dec Friday
6-Dec Saturday
7-Dec Sunday
8-Dec Monday
9-Dec Tuesday
10-DecWednesday
11-DecThursday
12-DecFriday
13-DecSaturday
14-DecSunday
15-DecMonday
16-DecTuesday
Target meetings:
1st one completed:
Primer Ordering Instructions (date?)
Everyone designs their primer - but we will only order one person's set.
Be sure you use the correct DNA Works output file to get your codon optimized DNA sequence (not just the CDS).
-- If you are use a Summer plate - you need to get your DNA Works Output file from Misc/Primers/DNAWorks_OutputSummer14
-- If you are use a Fall plate - you need to get your DNA Works Output file from Misc/Primers/DNAWorks_OutputFall14
Save the Word doc of your primer design into your GDocs
Print Word doc and paste into your Lab Notebook
Crosscheck your sequence with your Teammates
Put the sequences of the Tail Primers on your team's target page.
-- Enter your name for the person whose primers we will order - once you have designed the primers
Put the info and sequence on the Target Spreadsheet
https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodDJlZDlneXMtb1JuREV0MUZQYXU4YkE#gid=0
Order your primers
-- go to the ICMB core site (see our Targets Spreadsheet for the link)
-- find the IDT link
-- enter our username: VDS (all caps) and password: same as the password to get on to the laptops buildingname+labroomnumber
--Products/DNA/RNASynthesis/CustomDNAOligos
--select 2 for the Multiple Entry
-- leave defaults for Scale and Purification
-- enter your 2 primers and the Prefixes.
-- save to Wishlist, Dr. B will order when we have several of them.
25-Aug Monday
26-Aug Tuesday
27-Aug Wednesday
class
28-Aug Thursday
sign up for Fire Safety training (see link to left 'Required Lab Safety')
Lab times open for Nanodrop and Submit to DNA sequencing
Link to create dnaLIMS Account: (*must make an account before submitting DNA to sequencing)
http://146.6.133.14/cgi-bin/dna/loginNn.cgi
--- sign up on sheet above
Nanodrop protocol
Submit to DNA Sequencing
29-Aug Friday
30-Aug Saturday
31-Aug Sunday
25-Aug Monday
26-Aug Tuesday
27-Aug Wednesday
class
28-Aug Thursday
sign up for Fire Safety training (see link to left 'Required Lab Safety')
startup your cloning work again
29-Aug Friday
30-Aug Saturday
31-Aug Sunday
Be sure you have 8-10hrs/week
- for the 1st week of class that should be about 3-4hrs since the lab was only open for 2 days
For this week, you need about 6.5-8 hrs.
ITEMS TO DO THIS WEEK**
1-Sep Monday - LABOR DAY - no lab
2-Sep Tuesday
Transformation times at 3:30 PM (must start on time)
Make 500ml of LB and autoclave (with mentor)
3-Sep Wednesday
class
Transformation times at 3:30 PM (must start on time)
Make 500ml of LB and autoclave (with mentor)
4-Sep Thursday
Make 500ml of LB and autoclave (with mentor)
Dilute some primers (if they come in)
Transformation times at 5:30 PM (must start on time)
5-Sep Friday
1:30-4:30 pm Analyze DNA Sequence Exercise (as a group) OR Primer Design if Targets figured out
Make 500ml of LB and autoclave (with mentor)
Dilute some primers (if they come in)
6-Sep Saturday
Lab Notebook check - Saturday at 5pm
What Goes Where for notebook?:
Nanorop - 2 images for Wiki & protocol/images in Notebook
Submit to DNA - protocol in Notebook, if have result - put in Notebook too
Wet lab and virtual work should go into notebook
Oligo Design - upload output file to GDocs, paste Oligo sequence into your Target page, in Notebook too
Analyze DNA Sequence - upload results to GDocs (put the protocol in your Notebook - results can stay in GDocs)
RE Digest - if done
PCR & run on an agarose gel - images to Wiki & protocol/images in Notebook
7-Sep Sunday
Target page updates due - 9 pm - SKIP FOR THIS WEEK
Wikispaces posting due - 9 pm
Add content to YOUR research page on Wikispaces
Put a line and 'Week 1&2'
Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Wiki postings should be a sort of highlights of results page.
You should have nanodrop images, gel images, yields from protein purification, brief virtual results, etc.
You don't need alot of lengthy description of the procedures - only figure captions and a brief analysis of
the result (e.g. 1-2 sentences of why it did or didn't work, next steps, etc.).
You should have enough information in the captiont to let the reader (Dr. B) understand what it is.
Be sure you have 8-10hrs/week
- for the 1st week of class that should be about 3-4hrs since the lab was only open for 2 days
For this week, you need about 6.5-8 hrs.
1-Sep Monday
2-Sep Tuesday
3-Sep Wednesday
class
3-4 Zain & Hailey site specific training with Priya
4-Sep Thursday
5-Sep Friday
6-Sep Saturday
7-Sep Sunday
ITEMS TO DO THIS WEEK
Grow up DH5alpha cells for Plasmid Preps (just store pellets though - don't do MidiPrep yet):
4:00 - 5 PM - start overnight cultures of plasmids in DH5alpha for midi prepping later.-Grow up pNIC-Bsa4 overnight in 160ml of LB + Kan
--pNIC-Bsa4 is a 'low copy' plasmid
--spin down next morning
(save in -20degC or proceed to Midi-Prep - 2-3hrs)
-- if you don't' have time to spin down in morning (~30-45 min), you can
temporarily store your growth flask in 4degC for a few hours til you can spin it in the afternoon.
Pellets can be frozen and stored til next day or so.
In order to make lots of plasmid that we will need for cloning:
-- Plasmid Midi-prep (in pairs) - use Tony's new protocol
8-Sep Monday
9-Sep Tuesday
FIRE SAFETY TRAINING for FRI Students only
-- Speed Way in front of SAC (just show up and sign in)
Fill Out: Target Selection Form
https://docs.google.com/spreadsheet/viewform?formkey=dHJITzhKOHVvMUhNU05TRE81NktjV0E6MA
10-SepWednesday
class
Target Selection Form
11-SepThursday
Create/Update Target page on Wikispaces for your Team's target
Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall14.doc - 2 hrs
12-SepFriday
Create/Update Target page on Wikispaces for your Team's target
Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall14.doc - 2 hrs
13-SepSaturday
14-SepSunday
8-Sep Monday
9-Sep Tuesday
FIRE SAFETY TRAINING for FRI Students only
-- Speed Way in front of SAC (just show up and sign in)
10-SepWednesday
class
11-SepThursday
4- 8 pm PyMol Refresher Help Session in Computer Lab
12-SepFriday
PyMol Refresher due for Vets (less Zain, Hailey)
can count as 2 hours of lab time
13-SepSaturday
14-SepSunday
ITEMS TO DO THIS WEEK
Grow up pNIC-Bsa4 in DH5alpha cells for Plasmid Preps
4:00 - 5 PM - start overnight cultures of plasmids in DH5alpha for midi prepping later.-Grow up pNIC-Bsa4 overnight in 160ml of LB + Kan
--pNIC-Bsa4 is a 'low copy' plasmid
--spin down next morning (10-11 am) - make sure a mentor can be there!
(save in -20degC or proceed to Midi-Prep - 2-3hrs)
-- if you don't' have time to spin down in morning (~30-45 min), you can
temporarily store your growth flask in 4degC for a few hours til you can spin it in the afternoon.
Pellets can be frozen and stored til next day or so.
Not due yet, but Mid Semester Research Report Guidelines posted to:
GDocs/Results&Data/ResearchReport/
GuidelinesResearchReportonTarget_VDS_Fall14.doc
15-SepMonday
16-SepTuesday
17-SepWednesday
18-SepThursday
19-SepFriday
20-SepSaturday
Lab Notebook check - Saturday at 5pm
What Goes Where for notebook?:
Oligo Design - protocol and DNA Works output file
Analyze DNA Sequence
RE Digest
PCR & run on an agarose gel (if done)
21-SepSunday
Wikispaces posting due - 9 pm
Add content to YOUR research page on Wikispaces
Put a line and 'Week 3&4'
Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Wiki postings should be a sort of highlights of results page.
You should have nanodrop images, gel images, yields from protein purification, brief virtual results, etc.
You don't need alot of lengthy description of the procedures - only figure captions and a brief analysis of
the result (e.g. 1-2 sentences of why it did or didn't work, next steps, etc.).
You should have enough information in the caption to let the reader (Dr. B) understand what it is.
Wet Lab
Virtual Work
start Virtual Screening Refresher - see GDocs/Protocols/VirtualProtocols
Not due yet, but Mid Semester Research Report Guidelines posted to:
GDocs/Results&Data/ResearchReport/
GuidelinesResearchReportonTarget_VDS_Fall14.doc
15-SepMonday
16-SepTuesday
17-SepWednesday
18-SepThursday
Virtual Refresher Help Session
19-SepFriday
Virtual Refresher Help Session
20-SepSaturday
Lab Notebook check - Saturday at 5pm
21-SepSunday
Wikispaces posting due - 9 pm
This week or next (depends on your lab hours)
Not due yet, but Mid Semester Research Report Guidelines posted to:
GDocs/Results&Data/ResearchReport/
GuidelinesResearchReportonTarget_VDS_Fall14.doc
22-SepMonday
23-SepTuesday
24-SepWednesday
PyMol Refresher due for Springers (plus Zain and Hailey)
can count as 2 hours of lab time
25-SepThursday
26-SepFriday
27-SepSaturday
28-SepSunday
Target page updates due - 9 pm
Wet Lab
Virtual Work
- Begin Virtual Screening setup (see meeting times)
- create homology model if needed for your target
- ProtocolHomologyModelVDS_v?.doc
You don't have to do all of these protocols right away - but you should aim to have your Homology model created this week and have started on Control Ligands selection (the first part of the Virtual Screening Protocol).Protocol_LigandPrep_VDS_v1_?.docx
ProtocolVirtualScreenYOURTarget_VDS_??.doc
-- see the sign up spreadsheet above for times
Target Page - update yours with your team (the person who comes first on the list of names is the point person and delegates the work)
Not due yet, but Mid Semester Research Report Guidelines posted to:
GDocs/Results&Data/ResearchReport/
GuidelinesResearchReportonTarget_VDS_Fall14.d
22-SepMonday
23-SepTuesday
24-SepWednesday
Virtual Screening Refresher due for Vets
can count as 2 hours of lab time
(Zain & Hailey) do PyMol Refresher
25-SepThursday
26-SepFriday
27-SepSaturday
28-SepSunday
Target page updates due - 9 pm
LINK TO EDIT THE PAGE: Add your name to the time you want
Check the Mentor schedule to see when mentors will be present in lab to help you out.
Wet Lab
Virtual Work
Virtual Screening Refresher - start looking at will be due next week
29-SepMonday
30-SepTuesday
1-Oct Wednesday
2-Oct Thursday
3-Oct Friday
4-Oct Saturday
5-Oct Sunday
Mid Semester Research Report due (a.k.a. Report on your Target)
Guidelines posted to:
GDocs/Results&Data/ResearchReport/GuidelinesResearchReportonTarget_VDS_Fall14.doc
Cloning should be completed by end or September
Start Expression
Virtual Work
29-SepMonday
30-SepTuesday
1-Oct Wednesday
2-Oct Thursday
3-Oct Friday
4-Oct Saturday
Lab Notebook check - Saturdays at 5pm
5-Oct Sunday
Mid Semester Research Report due (a.k.a. Report on your Target)
Guidelines posted to:
GDocs/Results&Data/ResearchReport/GuidelinesResearchReportonTarget_VDS_Fall14.doc
Check the Mentor schedule to see when mentors
will be present in lab to help you out.
Wet Lab
- ProtocolPCR_PrimerOverlap
WithQ5Polymerase_VDS_Fall14.docxSecondary PCR trials
Virtual Work
Virtual Screening Refresher - due in 2 weeks from now
6-Oct Monday
7-Oct Tuesday
8-Oct Wednesday
9-Oct Thursday
10-OctFriday
11-OctSaturday
Lab Notebook check - Saturdays at 5pm
12-OctSunday
Wikispaces posting due - Sundays at 9 pm (For Weeks 5,6,7)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y&Z'
Virtual Work
- Control Ligands selection and LigPrep is due at end of week
- Beginning of the ProtocolVirtualScreenYOURTarget_VDS_Fall14.doc
- Protocol_LigandPrep_VDS_v1_6.docx
- Virtual Set up is due at end of week
- e.g homology model (if needed) and setting up protein in GOLD- analyze control ligands' scores
We will set up
6-Oct Monday
7-Oct Tuesday
8-Oct Wednesday
9-Oct Thursday
10-OctFriday
11-OctSaturday
Lab Notebook check - Saturdays at 5pm
12-OctSunday
Wikispaces posting due - Sundays at 9 pm (For Weeks 5,6,7)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y&Z'
Check the Mentor schedule to see when mentors will be present in lab to help you out.
We will also have some dedicated virtual screening help sessions (see below)
Wet Lab
- continue cloning work on your project
- start cutting your pNIC-Bsa4 while working on your PCRs
Virtual Work* Virtual Screening Refresher (can count as 4 hrs of wet lab time for the whole exercise)
13-OctMonday
5-7 pm Virtual Screening Help Session in wet lab
14-OctTuesday
15-OctWednesday
3-7 pm Virtual Screening Help Session in wet lab
16-OctThursday
4-7 pm Help Session for:
Virtual Screening & LICpNIC-Bsa4cloningExercise
17-OctFriday
2-6 PM Help Session for:
Virtual Screening & LICpNIC-Bsa4cloningExercise
18-OctSaturday
1- 4 PM Help Session for:
Virtual Screening & LICpNIC-Bsa4cloningExercise
Run1 of Virtual Screen Refresher due today
LICpNIC-Bsa4cloningExerciseVDS_Fall14 due today
19-OctSunday
Wet Lab
Virtual Work
- analyze control ligands' scores
- submit jobs for small screening libraries (cb306, NIHcc)
---InHouseCompounds (~40 ligs) -use 1 processor
---CB306 (306 ligs) - use 1 processor
---NIHClinicalCollection (446 ligs), use 1 processor
---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor
--- If those look good - submit CBDiversity (large library - ~50k)
13-OctMonday
14-OctTuesday
15-OctWednesday
16-OctThursday
17-OctFriday
18-OctSaturday
19-OctSunday
Check the Mentor schedule to see when mentors will be present in lab to help you out.
We will also have some dedicated virtual screening help sessions (see below)
Wet Lab
- continue cloning work on your project
- start cutting your pNIC-Bsa4 while working on your PCRs
- once PCR Squared is done - carry out cloning protocol
- ProtocolpNIC-Bsa4_cloningVDS_Fall14.doc
- make sucrose + kan plates if there aren't any (get a mentors help)
Virtual Work* Virtual Screening Refresher (can count as 4 hrs of wet lab time for the whole exercise)
20-OctMonday
21-OctTuesday
22-OctWednesday
23-OctThursday
24-OctFriday
25-OctSaturday
Virtual Screening Refresher - due
26-OctSunday
Peer Review of Mid Semester Research Report on target
--- see GDrive folder for instructions (
ResearchReport_Materials&Methods_Guidelines)
Wet Lab
Virtual Work
- analyze scores
- submit jobs for a large screening library (CB Diversity - 50k)
20-OctMonday
21-OctTuesday
22-OctWednesday
23-OctThursday
24-OctFriday
25-OctSaturday
26-OctSunday
Peer Review of Mid Semester Research Report on target
--- see GDrive folder for instructions (
ResearchReport_Materials&Methods_Guidelines)
Check the Mentor schedule to see when mentors will be present in lab to help you out.
We will also have some dedicated virtual screening help sessions (see below)
Wet Lab
Virtual Work
27-OctMonday
28-OctTuesday
29-OctWednesday - Journal Club
30-OctThursday
31-OctFriday
1-Nov Saturday
Lab Notebook Due at 5pm
2-Nov Sunday
Cloning Materials & Methods due
Wikispaces posting due - Sundays at 9 pm (For Weeks 8,9,10)
Add content to YOUR research page on Wikispaces
Put a line and 'Week 8, 9, and 10'
Enzyme Assays
Virtual Screening
- ChemBridge Diversity
Priority: Luis, Charina, Andee, Nikki, Andrei, Hailey
27-OctMonday
28-OctTuesday
29-OctWednesday - Journal Club
30-OctThursday
31-OctFriday
1-Nov Saturday
Lab Notebook Due at 5pm
2-Nov Sunday
Cloning Materials & Methods due
Wikispaces posting due - Sundays at 9 pm (For Weeks 8,9,10)
Add content to YOUR research page on Wikispaces
Put a line and 'Week 8, 9, and 10'
Check the Mentor schedule to see when mentors will be present in lab to help you out.
We will also have some dedicated virtual screening help sessions (see below)
Wet Lab
Virtual Work
3-Nov Monday
4-Nov Tuesday
5-Nov Wednesday
6-Nov Thursday
7-Nov Friday
8-Nov Saturday
9-Nov Sunday
Peer Review of M&M Cloning Due at m/n -
–You have 2 different people’s which you need to review
–Make 5 constructive criticisms
–Make 2 compliments
- make sure to add your Initials to each comment so we know who did what - JTB
Enzyme Assays
3-Nov Monday
4-Nov Tuesday
5-Nov Wednesday
6-Nov Thursday
7-Nov Friday
8-Nov Saturday
9-Nov Sunday
Peer Review of M&M Cloning Due at m/n
–You have 2 different people’s which you need to review
–Make 5 constructive criticisms
–Make 2 compliments
- make sure to add your Initials to each comment so we know who did what - JTB
Virtual Work
Virtual Work
10-NovMonday
11-NovTuesday
12-NovWednesday
no journal club this week
13-Nov Thursday
14-Nov Friday
15-NovSaturday
16-NovSunday
Virtual M&M due
Virtual Work
WEEK12
10-NovMonday
11-NovTuesday
12-NovWednesday
no journal club this week
13-Nov Thursday
14-Nov Friday
15-NovSaturday
16-NovSunday
Virtual M&M due
Virtual Work
- - analyze scores
- - continue screening small screening libraries (cb306, NIHcc, HF9)
- ---InHouseCompounds (~40 ligs) -use 1 processor
- ---CB306 (306 ligs) - use 1 processor
- ---NIHClinicalCollection (446 ligs), use 1 processor
- ---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor
17-Nov Monday18-Nov Tuesday
19-Nov Wednesday
Journal Club
20-Nov Thursday
21-Nov Friday
22-Nov Saturday
Lab Notebook Due at 5pm
23-Nov Sunday
Wikispaces posting due - Sundays at 9 pm (For Weeks 11,12,13)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y&Z'
Enzyme Assays & Inhibition Assays
Virtual Work
17-Nov Monday
18-Nov Tuesday
19-Nov Wednesday
Journal Club
20-Nov Thursday
21-Nov Friday
22-Nov Saturday
Lab Notebook Due at 5pm
23-Nov Sunday
Wikispaces posting due - Sundays at 9 pm (For Weeks 11,12,13)
Add content to YOUR research page on Wikispaces
Put a line and 'Week X&Y&Z'
do some virtual screening
Wet Lab work
we will have mentors on duty for Mon, Tues, Wed - so continue your cloning work if you are in town
WEEK14
24-Nov Monday
25-Nov Tuesday -
Peer Review of M&M Virtual Due at m/n
–You have 2 different people’s which you need to review
–Make 5 constructive criticisms
–Make 2 compliments
- make sure to add your Initials to each comment so we know who did what - JTB
Expression, Purification, Characterization M&M due (can also turn in on Sunday night (Nov 30th)
26-Nov Wednesday - NO CLASS (Thanksgiving Break)
We will have mentors on duty if you want to do lab work
27-Nov Thursday
28-Nov Friday
29-Nov Saturday
30-Nov Sunday
see above for Peer Review and M&M that are due
do some virtual screening
Wet Lab work
we will have mentors on duty for Mon, Tues, Wed
WEEK14
24-Nov Monday
25-Nov Tuesday
Peer Review of M&M Virtual Due at m/n
–You have 2 different people’s which you need to review
–Make 5 constructive criticisms
–Make 2 compliments
- make sure to add your Initials to each comment so we know who did what - JTB
Expression, Purification, Characterization M&M due
(can also turn in on Sunday night (Nov 30th)
26-Nov Wednesday - NO CLASS (Thanksgiving Break)
We will have mentors on duty if you want to do lab work
27-Nov Thursday
28-Nov Friday
29-Nov Saturday
30-Nov Sunday
see above for Peer Review and M&M that are due